noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.1.1.1.6) Plots of Abundance.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.1.1.1.6.2) Iterating over all combinations of grouping variables
(1.1.1.1.6.2.1) Grouping variables Sample.type,visit
(1.1.1.1.6.2.2) Iterating over Abundance. profile sorting order
(1.1.1.1.6.2.2.1) Abundance. profile sorting order: average abundance
(1.1.1.1.6.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.1.6.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.1.6.2.2.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.1.6.2.2.2.1.1.0) Table 6. Data table used for plots. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.1.6.2.2.2.1.1.0-3236b29748c.1.1.1.1.6.2.2.2.1.1.csv

.record.id Sample.type visit feature Abundance
SM1 patient 1 Bacteroidetes 0.7837908
SM10 patient 3 Bacteroidetes 0.2396904
SM100 patient 4 Bacteroidetes 0.5483424
SM11 patient 2 Bacteroidetes 0.9085606
SM12 patient 1 Bacteroidetes 0.9297539
SM13 patient 1 Bacteroidetes 0.7549107
SM14 patient 1 Bacteroidetes 0.0643696
SM15 control 1 Bacteroidetes 0.4787347
SM16 patient 4 Bacteroidetes 0.3909652
SM17 patient 1 Bacteroidetes 0.8191974
SM18 patient 2 Bacteroidetes 0.7196575
SM19 patient 2 Bacteroidetes 0.2253586
SM2 patient 1 Bacteroidetes 0.8869878
SM20 control 1 Bacteroidetes 0.5052377
SM21 patient 1 Bacteroidetes 0.5680175
SM22 patient 1 Bacteroidetes 0.6115163
SM23 patient 2 Bacteroidetes 0.2816259
SM24 patient 1 Bacteroidetes 0.8667524
SM25 patient 4 Bacteroidetes 0.4539656
SM26 control 1 Bacteroidetes 0.5339906
SM28 control 1 Bacteroidetes 0.2661871
SM29 patient 3 Bacteroidetes 0.9319131
SM3 patient 2 Bacteroidetes 0.3065958
SM30 patient 4 Bacteroidetes 0.0706857
SM31 control 2 Bacteroidetes 0.5825243
SM33 patient 1 Bacteroidetes 0.6904013
SM35 control 1 Bacteroidetes 0.6847011
SM36 patient 4 Bacteroidetes 0.0003219
SM37 control 1 Bacteroidetes 0.4116736
SM38 patient 2 Bacteroidetes 0.9844826
SM39 patient 1 Bacteroidetes 0.9344382
SM40 patient 4 Bacteroidetes 0.7285173
SM41 patient 1 Bacteroidetes 0.5561997
SM42 patient 4 Bacteroidetes 0.7113608
SM43 patient 4 Bacteroidetes 0.7229302
SM44 control 1 Bacteroidetes 0.3689400
SM45 patient 2 Bacteroidetes 0.0000000
SM48 control 1 Bacteroidetes 0.7198795
SM49 patient 1 Bacteroidetes 0.9321676
SM5 patient 3 Bacteroidetes 0.8376844
SM50 patient 3 Bacteroidetes 0.0000000
SM51 patient 4 Bacteroidetes 0.7147000
SM52 patient 1 Bacteroidetes 0.0982678
SM53 patient 2 Bacteroidetes 0.8029344
SM54 patient 3 Bacteroidetes 0.8090072
SM55 control 1 Bacteroidetes 0.7867457
SM56 patient 2 Bacteroidetes 0.7317232
SM57 patient 1 Bacteroidetes 0.9046076
SM58 patient 2 Bacteroidetes 0.7734046
SM59 patient 3 Bacteroidetes 0.0576779
SM60 patient 3 Bacteroidetes 0.8495575
SM62 patient 1 Bacteroidetes 0.9714974
SM63 control 1 Bacteroidetes 0.6522523
SM64 patient 2 Bacteroidetes 0.8682775
SM65 patient 3 Bacteroidetes 0.3740898
SM66 control 1 Bacteroidetes 0.6462271
SM67 patient 4 Bacteroidetes 0.9138286
SM68 patient 4 Bacteroidetes 0.1704581
SM69 patient 4 Bacteroidetes 0.8374262
SM7 control 1 Bacteroidetes 0.2200704
SM70 control 1 Bacteroidetes 0.5636549
SM71 patient 3 Bacteroidetes 0.9181355
SM72 control 1 Bacteroidetes 0.2780423
SM73 patient 1 Bacteroidetes 0.8563497
SM74 control 2 Bacteroidetes 0.0926350
SM75 patient 3 Bacteroidetes 0.0023769
SM76 control 1 Bacteroidetes 0.8226714
SM77 patient 2 Bacteroidetes 0.7635462
SM79 patient 2 Bacteroidetes 0.8495792
SM8 patient 1 Bacteroidetes 0.8249907
SM81 control 1 Bacteroidetes 0.0000000
SM82 patient 4 Bacteroidetes 0.9557214
SM83 patient 1 Bacteroidetes 0.8253707
SM84 patient 1 Bacteroidetes 0.8861386
SM86 patient 2 Bacteroidetes 0.0034130
SM87 patient 1 Bacteroidetes 0.8668189
SM88 patient 2 Bacteroidetes 0.8387042
SM89 control 1 Bacteroidetes 0.8860391
SM9 patient 2 Bacteroidetes 0.6635130
SM90 patient 2 Bacteroidetes 0.6175743
SM91 patient 3 Bacteroidetes 0.7223533
SM92 patient 3 Bacteroidetes 0.8864163
SM93 patient 1 Bacteroidetes 0.7781065
SM95 control 1 Bacteroidetes 0.5376651
SM96 patient 1 Bacteroidetes 0.6381524
SM98 patient 3 Bacteroidetes 0.8378232
SM99 patient 3 Bacteroidetes 0.6950886
SM1 patient 1 Firmicutes 0.1926574
SM10 patient 3 Firmicutes 0.7267041
SM100 patient 4 Firmicutes 0.4106607
SM11 patient 2 Firmicutes 0.0832883
SM12 patient 1 Firmicutes 0.0667050
SM13 patient 1 Firmicutes 0.2004464
SM14 patient 1 Firmicutes 0.8985233
SM15 control 1 Firmicutes 0.5021584
SM16 patient 4 Firmicutes 0.5901852
SM17 patient 1 Firmicutes 0.1419115
SM18 patient 2 Firmicutes 0.2613732
SM19 patient 2 Firmicutes 0.7376215
SM2 patient 1 Firmicutes 0.1035274
SM20 control 1 Firmicutes 0.4700510
SM21 patient 1 Firmicutes 0.4124769
SM22 patient 1 Firmicutes 0.3619962
SM23 patient 2 Firmicutes 0.7183741
SM24 patient 1 Firmicutes 0.0873312
SM25 patient 4 Firmicutes 0.5346644
SM26 control 1 Firmicutes 0.4376724
SM28 control 1 Firmicutes 0.6702638
SM29 patient 3 Firmicutes 0.0659983
SM3 patient 2 Firmicutes 0.6836746
SM30 patient 4 Firmicutes 0.6301592
SM31 control 2 Firmicutes 0.3685275
SM33 patient 1 Firmicutes 0.0664831
SM35 control 1 Firmicutes 0.1777677
SM36 patient 4 Firmicutes 0.9916318
SM37 control 1 Firmicutes 0.5380090
SM38 patient 2 Firmicutes 0.0149522
SM39 patient 1 Firmicutes 0.0457112
SM40 patient 4 Firmicutes 0.1850893
SM41 patient 1 Firmicutes 0.2222222
SM42 patient 4 Firmicutes 0.2680816
SM43 patient 4 Firmicutes 0.2170803
SM44 control 1 Firmicutes 0.5480690
SM45 patient 2 Firmicutes 0.9998080
SM48 control 1 Firmicutes 0.2306368
SM49 patient 1 Firmicutes 0.0630087
SM5 patient 3 Firmicutes 0.1042550
SM50 patient 3 Firmicutes 0.9071785
SM51 patient 4 Firmicutes 0.2014276
SM52 patient 1 Firmicutes 0.7350474
SM53 patient 2 Firmicutes 0.1567175
SM54 patient 3 Firmicutes 0.1867193
SM55 control 1 Firmicutes 0.1964930
SM56 patient 2 Firmicutes 0.2457572
SM57 patient 1 Firmicutes 0.0910727
SM58 patient 2 Firmicutes 0.2163913
SM59 patient 3 Firmicutes 0.9138577
SM60 patient 3 Firmicutes 0.0667120
SM62 patient 1 Firmicutes 0.0272983
SM63 control 1 Firmicutes 0.3144144
SM64 patient 2 Firmicutes 0.0731544
SM65 patient 3 Firmicutes 0.5987086
SM66 control 1 Firmicutes 0.3329670
SM67 patient 4 Firmicutes 0.0858185
SM68 patient 4 Firmicutes 0.7067622
SM69 patient 4 Firmicutes 0.1394156
SM7 control 1 Firmicutes 0.6870599
SM70 control 1 Firmicutes 0.3690709
SM71 patient 3 Firmicutes 0.0709753
SM72 control 1 Firmicutes 0.6537037
SM73 patient 1 Firmicutes 0.1129618
SM74 control 2 Firmicutes 0.8235679
SM75 patient 3 Firmicutes 0.9925297
SM76 control 1 Firmicutes 0.1656713
SM77 patient 2 Firmicutes 0.2001802
SM79 patient 2 Firmicutes 0.1429830
SM8 patient 1 Firmicutes 0.1345940
SM81 control 1 Firmicutes 0.4655685
SM82 patient 4 Firmicutes 0.0404868
SM83 patient 1 Firmicutes 0.1639209
SM84 patient 1 Firmicutes 0.0789167
SM86 patient 2 Firmicutes 0.9748681
SM87 patient 1 Firmicutes 0.0711568
SM88 patient 2 Firmicutes 0.1293265
SM89 control 1 Firmicutes 0.0789706
SM9 patient 2 Firmicutes 0.2900041
SM90 patient 2 Firmicutes 0.3494224
SM91 patient 3 Firmicutes 0.2239015
SM92 patient 3 Firmicutes 0.0989801
SM93 patient 1 Firmicutes 0.2169177
SM95 control 1 Firmicutes 0.3980721
SM96 patient 1 Firmicutes 0.2489554
SM98 patient 3 Firmicutes 0.0793432
SM99 patient 3 Firmicutes 0.2789868
SM1 patient 1 Proteobacteria 0.0219067
SM10 patient 3 Proteobacteria 0.0063606
SM100 patient 4 Proteobacteria 0.0290747
SM11 patient 2 Proteobacteria 0.0032064
SM12 patient 1 Proteobacteria 0.0011951
SM13 patient 1 Proteobacteria 0.0049107
SM14 patient 1 Proteobacteria 0.0064370
SM15 control 1 Proteobacteria 0.0124549
SM16 patient 4 Proteobacteria 0.0053624
SM17 patient 1 Proteobacteria 0.0223417
SM18 patient 2 Proteobacteria 0.0167870
SM19 patient 2 Proteobacteria 0.0356317
SM2 patient 1 Proteobacteria 0.0056413
SM20 control 1 Proteobacteria 0.0021488
SM21 patient 1 Proteobacteria 0.0131159
SM22 patient 1 Proteobacteria 0.0122841
SM23 patient 2 Proteobacteria 0.0000000
SM24 patient 1 Proteobacteria 0.0415434
SM25 patient 4 Proteobacteria 0.0030505
SM26 control 1 Proteobacteria 0.0053778
SM28 control 1 Proteobacteria 0.0171863
SM29 patient 3 Proteobacteria 0.0000000
SM3 patient 2 Proteobacteria 0.0069012
SM30 patient 4 Proteobacteria 0.2575561
SM31 control 2 Proteobacteria 0.0024272
SM33 patient 1 Proteobacteria 0.2423289

(1.1.1.1.6.2.2.2.1.1.1) Widget 2. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.1.6.2.2.2.1.1.1-323b8036cfDynamic.Pivot.Table.html

(1.1.1.1.6.2.2.2.1.1.1) Widget 3. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.1.6.2.2.2.1.1.1-3234f489b67Dynamic.Pivot.Table.html

(1.1.1.1.6.2.2.2.1.1.1) Table 7. Summary table. Data grouped by Sample.type,visit. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.1.6.2.2.2.1.1.1-32364869b99.1.1.1.1.6.2.2.2.1.1.csv

feature Sample.type visit mean sd median incidence
Bacteroidetes control 1 5.202e-01 0.2325637 0.5358279 0.94444
Bacteroidetes control 2 3.376e-01 0.3464040 0.3375796 1.00000
Bacteroidetes patient 1 7.413e-01 0.2398308 0.8249907 1.00000
Bacteroidetes patient 2 6.082e-01 0.3173005 0.7317232 0.94118
Bacteroidetes patient 3 5.830e-01 0.3642181 0.7656803 0.92857
Bacteroidetes patient 4 5.553e-01 0.3168360 0.7113608 1.00000
Firmicutes control 1 4.020e-01 0.1834321 0.4178722 1.00000
Firmicutes control 2 5.960e-01 0.3217622 0.5960477 1.00000
Firmicutes patient 1 2.063e-01 0.2171699 0.1345940 1.00000
Firmicutes patient 2 3.693e-01 0.3216403 0.2457572 1.00000
Firmicutes patient 3 3.796e-01 0.3632886 0.2053104 1.00000
Firmicutes patient 4 3.847e-01 0.2858955 0.2680816 1.00000
Proteobacteria control 1 4.251e-02 0.0735425 0.0176317 1.00000
Proteobacteria control 2 1.152e-02 0.0128656 0.0115246 1.00000
Proteobacteria patient 1 3.006e-02 0.0571305 0.0122841 0.95652
Proteobacteria patient 2 1.901e-02 0.0174805 0.0167870 0.94118
Proteobacteria patient 3 2.157e-02 0.0267913 0.0091310 0.92857
Proteobacteria patient 4 5.151e-02 0.0716240 0.0217594 0.92308
Unclassified_Bacteria control 1 1.364e-02 0.0114079 0.0105404 1.00000
Unclassified_Bacteria control 2 2.617e-02 0.0324305 0.0261680 1.00000
Unclassified_Bacteria patient 1 8.586e-03 0.0185047 0.0036576 0.95652
Unclassified_Bacteria patient 2 2.162e-03 0.0019168 0.0019582 0.88235
Unclassified_Bacteria patient 3 3.391e-03 0.0031220 0.0024169 1.00000
Unclassified_Bacteria patient 4 4.709e-03 0.0065490 0.0014149 1.00000
Actinobacteria control 1 1.734e-02 0.0449262 0.0027265 0.94444
Actinobacteria control 2 7.317e-03 0.0086317 0.0073171 1.00000
Actinobacteria patient 1 3.082e-03 0.0065802 0.0007416 0.86957
Actinobacteria patient 2 9.481e-04 0.0020047 0.0002227 0.76471
Actinobacteria patient 3 4.829e-03 0.0081190 0.0007112 0.71429
Actinobacteria patient 4 3.295e-03 0.0053213 0.0006658 0.69231
Verrucomicrobia control 1 2.550e-03 0.0051198 0.0000000 0.38889
Verrucomicrobia control 2 2.136e-02 0.0292859 0.0213629 1.00000
Verrucomicrobia patient 1 1.056e-02 0.0368541 0.0000000 0.34783
Verrucomicrobia patient 2 3.903e-04 0.0011122 0.0000000 0.11765
Verrucomicrobia patient 3 5.727e-04 0.0018438 0.0000000 0.14286
Verrucomicrobia patient 4 2.846e-05 0.0001026 0.0000000 0.07692

(1.1.1.1.6.2.2.2.1.1.1) Figure 5. Abundance. Data grouped by Sample.type,visit. bar_stacked plot. Image file: plots/3235e711569.svg.

(1.1.1.1.6.2.2.2.1.1.1) Figure 6. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/3232df4e96.svg.

(1.1.1.1.6.2.2.2.1.1.1) Figure 7. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3231b96a55.svg.

(1.1.1.1.6.2.2.2.1.1.1) Figure 8. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323d7040a2.svg.

(1.1.1.1.6.2.2.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.1.6.2.2.2.1.2.1) Figure 9. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32361b9cdf5.svg.

(1.1.1.1.6.2.2.2.1.2.1) Figure 10. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323605fd3f4.svg.

(1.1.1.1.6.2.2.2.1.2.1) Figure 11. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32314a8f6d9.svg.

(1.1.1.1.6.2.2.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.1.6.2.2.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.1.6.2.2.2.2.1.1) Figure 12. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323d17b05f.svg.

(1.1.1.1.6.2.2.2.2.1.1) Figure 13. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3235afb5e67.svg.

(1.1.1.1.6.2.2.2.2.1.1) Figure 14. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/3237d1d1426.svg.

(1.1.1.1.6.2.2.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.1.6.2.2.2.2.2.1) Figure 15. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/3235068b188.svg.

(1.1.1.1.6.2.2.2.2.2.1) Figure 16. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323185e1645.svg.

(1.1.1.1.6.2.2.2.2.2.1) Figure 17. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/3235e8aeafe.svg.

(1.1.1.1.6.2.3) Grouping variables Sample.type.Drug.Before,visit
(1.1.1.1.6.2.4) Iterating over Abundance. profile sorting order
(1.1.1.1.6.2.4.1) Abundance. profile sorting order: average abundance
(1.1.1.1.6.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.1.6.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.1.6.2.4.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.1.6.2.4.2.1.1.0) Table 8. Data table used for plots. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.1.6.2.4.2.1.1.0-3232e59c40.1.1.1.1.6.2.4.2.1.1.csv

.record.id Sample.type.Drug.Before visit feature Abundance
SM1 patient TRUE . 1 Bacteroidetes 0.7837908
SM10 patient TRUE . 3 Bacteroidetes 0.2396904
SM100 patient TRUE . 4 Bacteroidetes 0.5483424
SM11 patient TRUE . 2 Bacteroidetes 0.9085606
SM12 patient TRUE . 1 Bacteroidetes 0.9297539
SM13 patient FALSE . 1 Bacteroidetes 0.7549107
SM14 patient FALSE . 1 Bacteroidetes 0.0643696
SM15 1 1 Bacteroidetes 0.4787347
SM16 patient FALSE . 4 Bacteroidetes 0.3909652
SM17 patient TRUE . 1 Bacteroidetes 0.8191974
SM18 patient FALSE . 2 Bacteroidetes 0.7196575
SM19 patient FALSE . 2 Bacteroidetes 0.2253586
SM2 patient FALSE . 1 Bacteroidetes 0.8869878
SM20 1 1 Bacteroidetes 0.5052377
SM21 patient FALSE . 1 Bacteroidetes 0.5680175
SM22 patient TRUE . 1 Bacteroidetes 0.6115163
SM23 patient TRUE . 2 Bacteroidetes 0.2816259
SM24 patient FALSE . 1 Bacteroidetes 0.8667524
SM25 patient FALSE . 4 Bacteroidetes 0.4539656
SM26 1 1 Bacteroidetes 0.5339906
SM28 1 1 Bacteroidetes 0.2661871
SM29 patient TRUE . 3 Bacteroidetes 0.9319131
SM3 patient TRUE . 2 Bacteroidetes 0.3065958
SM30 patient TRUE . 4 Bacteroidetes 0.0706857
SM31 1 2 Bacteroidetes 0.5825243
SM33 patient TRUE . 1 Bacteroidetes 0.6904013
SM35 1 1 Bacteroidetes 0.6847011
SM36 patient FALSE . 4 Bacteroidetes 0.0003219
SM37 1 1 Bacteroidetes 0.4116736
SM38 patient TRUE . 2 Bacteroidetes 0.9844826
SM39 patient FALSE . 1 Bacteroidetes 0.9344382
SM40 patient FALSE . 4 Bacteroidetes 0.7285173
SM41 patient TRUE . 1 Bacteroidetes 0.5561997
SM42 patient FALSE . 4 Bacteroidetes 0.7113608
SM43 patient TRUE . 4 Bacteroidetes 0.7229302
SM44 1 1 Bacteroidetes 0.3689400
SM45 patient FALSE . 2 Bacteroidetes 0.0000000
SM48 1 1 Bacteroidetes 0.7198795
SM49 patient TRUE . 1 Bacteroidetes 0.9321676
SM5 patient TRUE . 3 Bacteroidetes 0.8376844
SM50 patient FALSE . 3 Bacteroidetes 0.0000000
SM51 patient TRUE . 4 Bacteroidetes 0.7147000
SM52 patient FALSE . 1 Bacteroidetes 0.0982678
SM53 patient TRUE . 2 Bacteroidetes 0.8029344
SM54 patient TRUE . 3 Bacteroidetes 0.8090072
SM55 1 1 Bacteroidetes 0.7867457
SM56 patient TRUE . 2 Bacteroidetes 0.7317232
SM57 patient TRUE . 1 Bacteroidetes 0.9046076
SM58 patient FALSE . 2 Bacteroidetes 0.7734046
SM59 patient FALSE . 3 Bacteroidetes 0.0576779
SM60 patient TRUE . 3 Bacteroidetes 0.8495575
SM62 patient TRUE . 1 Bacteroidetes 0.9714974
SM63 1 1 Bacteroidetes 0.6522523
SM64 patient TRUE . 2 Bacteroidetes 0.8682775
SM65 patient TRUE . 3 Bacteroidetes 0.3740898
SM66 1 1 Bacteroidetes 0.6462271
SM67 patient TRUE . 4 Bacteroidetes 0.9138286
SM68 patient FALSE . 4 Bacteroidetes 0.1704581
SM69 patient TRUE . 4 Bacteroidetes 0.8374262
SM7 1 1 Bacteroidetes 0.2200704
SM70 1 1 Bacteroidetes 0.5636549
SM71 patient TRUE . 3 Bacteroidetes 0.9181355
SM72 1 1 Bacteroidetes 0.2780423
SM73 patient FALSE . 1 Bacteroidetes 0.8563497
SM74 1 2 Bacteroidetes 0.0926350
SM75 patient FALSE . 3 Bacteroidetes 0.0023769
SM76 1 1 Bacteroidetes 0.8226714
SM77 patient TRUE . 2 Bacteroidetes 0.7635462
SM79 patient FALSE . 2 Bacteroidetes 0.8495792
SM8 patient FALSE . 1 Bacteroidetes 0.8249907
SM81 1 1 Bacteroidetes 0.0000000
SM82 patient TRUE . 4 Bacteroidetes 0.9557214
SM83 patient TRUE . 1 Bacteroidetes 0.8253707
SM84 patient TRUE . 1 Bacteroidetes 0.8861386
SM86 patient TRUE . 2 Bacteroidetes 0.0034130
SM87 patient TRUE . 1 Bacteroidetes 0.8668189
SM88 patient TRUE . 2 Bacteroidetes 0.8387042
SM89 1 1 Bacteroidetes 0.8860391
SM9 patient FALSE . 2 Bacteroidetes 0.6635130
SM90 patient FALSE . 2 Bacteroidetes 0.6175743
SM91 patient TRUE . 3 Bacteroidetes 0.7223533
SM92 patient FALSE . 3 Bacteroidetes 0.8864163
SM93 patient TRUE . 1 Bacteroidetes 0.7781065
SM95 1 1 Bacteroidetes 0.5376651
SM96 patient FALSE . 1 Bacteroidetes 0.6381524
SM98 patient FALSE . 3 Bacteroidetes 0.8378232
SM99 patient FALSE . 3 Bacteroidetes 0.6950886
SM1 patient TRUE . 1 Firmicutes 0.1926574
SM10 patient TRUE . 3 Firmicutes 0.7267041
SM100 patient TRUE . 4 Firmicutes 0.4106607
SM11 patient TRUE . 2 Firmicutes 0.0832883
SM12 patient TRUE . 1 Firmicutes 0.0667050
SM13 patient FALSE . 1 Firmicutes 0.2004464
SM14 patient FALSE . 1 Firmicutes 0.8985233
SM15 1 1 Firmicutes 0.5021584
SM16 patient FALSE . 4 Firmicutes 0.5901852
SM17 patient TRUE . 1 Firmicutes 0.1419115
SM18 patient FALSE . 2 Firmicutes 0.2613732
SM19 patient FALSE . 2 Firmicutes 0.7376215
SM2 patient FALSE . 1 Firmicutes 0.1035274
SM20 1 1 Firmicutes 0.4700510
SM21 patient FALSE . 1 Firmicutes 0.4124769
SM22 patient TRUE . 1 Firmicutes 0.3619962
SM23 patient TRUE . 2 Firmicutes 0.7183741
SM24 patient FALSE . 1 Firmicutes 0.0873312
SM25 patient FALSE . 4 Firmicutes 0.5346644
SM26 1 1 Firmicutes 0.4376724
SM28 1 1 Firmicutes 0.6702638
SM29 patient TRUE . 3 Firmicutes 0.0659983
SM3 patient TRUE . 2 Firmicutes 0.6836746
SM30 patient TRUE . 4 Firmicutes 0.6301592
SM31 1 2 Firmicutes 0.3685275
SM33 patient TRUE . 1 Firmicutes 0.0664831
SM35 1 1 Firmicutes 0.1777677
SM36 patient FALSE . 4 Firmicutes 0.9916318
SM37 1 1 Firmicutes 0.5380090
SM38 patient TRUE . 2 Firmicutes 0.0149522
SM39 patient FALSE . 1 Firmicutes 0.0457112
SM40 patient FALSE . 4 Firmicutes 0.1850893
SM41 patient TRUE . 1 Firmicutes 0.2222222
SM42 patient FALSE . 4 Firmicutes 0.2680816
SM43 patient TRUE . 4 Firmicutes 0.2170803
SM44 1 1 Firmicutes 0.5480690
SM45 patient FALSE . 2 Firmicutes 0.9998080
SM48 1 1 Firmicutes 0.2306368
SM49 patient TRUE . 1 Firmicutes 0.0630087
SM5 patient TRUE . 3 Firmicutes 0.1042550
SM50 patient FALSE . 3 Firmicutes 0.9071785
SM51 patient TRUE . 4 Firmicutes 0.2014276
SM52 patient FALSE . 1 Firmicutes 0.7350474
SM53 patient TRUE . 2 Firmicutes 0.1567175
SM54 patient TRUE . 3 Firmicutes 0.1867193
SM55 1 1 Firmicutes 0.1964930
SM56 patient TRUE . 2 Firmicutes 0.2457572
SM57 patient TRUE . 1 Firmicutes 0.0910727
SM58 patient FALSE . 2 Firmicutes 0.2163913
SM59 patient FALSE . 3 Firmicutes 0.9138577
SM60 patient TRUE . 3 Firmicutes 0.0667120
SM62 patient TRUE . 1 Firmicutes 0.0272983
SM63 1 1 Firmicutes 0.3144144
SM64 patient TRUE . 2 Firmicutes 0.0731544
SM65 patient TRUE . 3 Firmicutes 0.5987086
SM66 1 1 Firmicutes 0.3329670
SM67 patient TRUE . 4 Firmicutes 0.0858185
SM68 patient FALSE . 4 Firmicutes 0.7067622
SM69 patient TRUE . 4 Firmicutes 0.1394156
SM7 1 1 Firmicutes 0.6870599
SM70 1 1 Firmicutes 0.3690709
SM71 patient TRUE . 3 Firmicutes 0.0709753
SM72 1 1 Firmicutes 0.6537037
SM73 patient FALSE . 1 Firmicutes 0.1129618
SM74 1 2 Firmicutes 0.8235679
SM75 patient FALSE . 3 Firmicutes 0.9925297
SM76 1 1 Firmicutes 0.1656713
SM77 patient TRUE . 2 Firmicutes 0.2001802
SM79 patient FALSE . 2 Firmicutes 0.1429830
SM8 patient FALSE . 1 Firmicutes 0.1345940
SM81 1 1 Firmicutes 0.4655685
SM82 patient TRUE . 4 Firmicutes 0.0404868
SM83 patient TRUE . 1 Firmicutes 0.1639209
SM84 patient TRUE . 1 Firmicutes 0.0789167
SM86 patient TRUE . 2 Firmicutes 0.9748681
SM87 patient TRUE . 1 Firmicutes 0.0711568
SM88 patient TRUE . 2 Firmicutes 0.1293265
SM89 1 1 Firmicutes 0.0789706
SM9 patient FALSE . 2 Firmicutes 0.2900041
SM90 patient FALSE . 2 Firmicutes 0.3494224
SM91 patient TRUE . 3 Firmicutes 0.2239015
SM92 patient FALSE . 3 Firmicutes 0.0989801
SM93 patient TRUE . 1 Firmicutes 0.2169177
SM95 1 1 Firmicutes 0.3980721
SM96 patient FALSE . 1 Firmicutes 0.2489554
SM98 patient FALSE . 3 Firmicutes 0.0793432
SM99 patient FALSE . 3 Firmicutes 0.2789868
SM1 patient TRUE . 1 Proteobacteria 0.0219067
SM10 patient TRUE . 3 Proteobacteria 0.0063606
SM100 patient TRUE . 4 Proteobacteria 0.0290747
SM11 patient TRUE . 2 Proteobacteria 0.0032064
SM12 patient TRUE . 1 Proteobacteria 0.0011951
SM13 patient FALSE . 1 Proteobacteria 0.0049107
SM14 patient FALSE . 1 Proteobacteria 0.0064370
SM15 1 1 Proteobacteria 0.0124549
SM16 patient FALSE . 4 Proteobacteria 0.0053624
SM17 patient TRUE . 1 Proteobacteria 0.0223417
SM18 patient FALSE . 2 Proteobacteria 0.0167870
SM19 patient FALSE . 2 Proteobacteria 0.0356317
SM2 patient FALSE . 1 Proteobacteria 0.0056413
SM20 1 1 Proteobacteria 0.0021488
SM21 patient FALSE . 1 Proteobacteria 0.0131159
SM22 patient TRUE . 1 Proteobacteria 0.0122841
SM23 patient TRUE . 2 Proteobacteria 0.0000000
SM24 patient FALSE . 1 Proteobacteria 0.0415434
SM25 patient FALSE . 4 Proteobacteria 0.0030505
SM26 1 1 Proteobacteria 0.0053778
SM28 1 1 Proteobacteria 0.0171863
SM29 patient TRUE . 3 Proteobacteria 0.0000000
SM3 patient TRUE . 2 Proteobacteria 0.0069012
SM30 patient TRUE . 4 Proteobacteria 0.2575561
SM31 1 2 Proteobacteria 0.0024272
SM33 patient TRUE . 1 Proteobacteria 0.2423289

(1.1.1.1.6.2.4.2.1.1.1) Widget 4. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.1.6.2.4.2.1.1.1-32343e976f9Dynamic.Pivot.Table.html

(1.1.1.1.6.2.4.2.1.1.1) Widget 5. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.1.6.2.4.2.1.1.1-32369d9ba89Dynamic.Pivot.Table.html

(1.1.1.1.6.2.4.2.1.1.1) Table 9. Summary table. Data grouped by Sample.type.Drug.Before,visit. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.1.6.2.4.2.1.1.1-32344d8b1c0.1.1.1.1.6.2.4.2.1.1.csv

feature Sample.type.Drug.Before visit mean sd median incidence
Bacteroidetes 1 1 5.202e-01 0.2325637 0.5358279 0.9444
Bacteroidetes 1 2 3.376e-01 0.3464040 0.3375796 1.0000
Bacteroidetes patient FALSE . 1 6.493e-01 0.3201539 0.7899507 1.0000
Bacteroidetes patient FALSE . 2 5.499e-01 0.3145855 0.6635130 0.8571
Bacteroidetes patient FALSE . 3 4.132e-01 0.4357994 0.3763832 0.8333
Bacteroidetes patient FALSE . 4 4.093e-01 0.2897517 0.4224654 1.0000
Bacteroidetes patient TRUE . 1 8.120e-01 0.1269555 0.8253707 1.0000
Bacteroidetes patient TRUE . 2 6.490e-01 0.3294165 0.7832403 1.0000
Bacteroidetes patient TRUE . 3 7.103e-01 0.2597599 0.8233458 1.0000
Bacteroidetes patient TRUE . 4 6.805e-01 0.3019724 0.7229302 1.0000
Firmicutes 1 1 4.020e-01 0.1834321 0.4178722 1.0000
Firmicutes 1 2 5.960e-01 0.3217622 0.5960477 1.0000
Firmicutes patient FALSE . 1 2.980e-01 0.2950437 0.1675202 1.0000
Firmicutes patient FALSE . 2 4.282e-01 0.3167081 0.2900041 1.0000
Firmicutes patient FALSE . 3 5.451e-01 0.4368169 0.5930827 1.0000
Firmicutes patient FALSE . 4 5.461e-01 0.2946212 0.5624248 1.0000
Firmicutes patient TRUE . 1 1.357e-01 0.0936925 0.0910727 1.0000
Firmicutes patient TRUE . 2 3.280e-01 0.3353397 0.1784489 1.0000
Firmicutes patient TRUE . 3 2.555e-01 0.2602282 0.1454871 1.0000
Firmicutes patient TRUE . 4 2.464e-01 0.2068684 0.2014276 1.0000
Proteobacteria 1 1 4.251e-02 0.0735425 0.0176317 1.0000
Proteobacteria 1 2 1.152e-02 0.0128656 0.0115246 1.0000
Proteobacteria patient FALSE . 1 2.732e-02 0.0473340 0.0119343 1.0000
Proteobacteria patient FALSE . 2 1.851e-02 0.0163312 0.0167870 1.0000
Proteobacteria patient FALSE . 3 2.796e-02 0.0331289 0.0116967 1.0000
Proteobacteria patient FALSE . 4 3.770e-02 0.0459902 0.0129398 1.0000
Proteobacteria patient TRUE . 1 3.216e-02 0.0655164 0.0122841 0.9231
Proteobacteria patient TRUE . 2 1.937e-02 0.0191073 0.0138488 0.9000
Proteobacteria patient TRUE . 3 1.677e-02 0.0220834 0.0070957 0.8750
Proteobacteria patient TRUE . 4 6.335e-02 0.0902400 0.0290747 0.8571
Unclassified_Bacteria 1 1 1.364e-02 0.0114079 0.0105404 1.0000
Unclassified_Bacteria 1 2 2.617e-02 0.0324305 0.0261680 1.0000
Unclassified_Bacteria patient FALSE . 1 1.480e-02 0.0271664 0.0044485 1.0000
Unclassified_Bacteria patient FALSE . 2 2.186e-03 0.0022072 0.0013882 0.8571
Unclassified_Bacteria patient FALSE . 3 5.270e-03 0.0038238 0.0034445 1.0000
Unclassified_Bacteria patient FALSE . 4 4.114e-03 0.0042506 0.0020074 1.0000
Unclassified_Bacteria patient TRUE . 1 3.807e-03 0.0041644 0.0022574 0.9231
Unclassified_Bacteria patient TRUE . 2 2.145e-03 0.0018121 0.0020539 0.9000
Unclassified_Bacteria patient TRUE . 3 1.982e-03 0.0015373 0.0013446 1.0000
Unclassified_Bacteria patient TRUE . 4 5.219e-03 0.0083704 0.0013988 1.0000
Actinobacteria 1 1 1.734e-02 0.0449262 0.0027265 0.9444
Actinobacteria 1 2 7.317e-03 0.0086317 0.0073171 1.0000
Actinobacteria patient FALSE . 1 3.471e-03 0.0076244 0.0008172 1.0000
Actinobacteria patient FALSE . 2 7.392e-04 0.0011806 0.0002936 0.7143
Actinobacteria patient FALSE . 3 3.698e-03 0.0074005 0.0007112 0.6667
Actinobacteria patient FALSE . 4 2.476e-03 0.0042882 0.0004254 0.6667
Actinobacteria patient TRUE . 1 2.782e-03 0.0059632 0.0006927 0.7692
Actinobacteria patient TRUE . 2 1.094e-03 0.0024815 0.0002192 0.8000
Actinobacteria patient TRUE . 3 5.677e-03 0.0090211 0.0010307 0.7500
Actinobacteria patient TRUE . 4 3.997e-03 0.0063296 0.0006692 0.7143
Verrucomicrobia 1 1 2.550e-03 0.0051198 0.0000000 0.3889
Verrucomicrobia 1 2 2.136e-02 0.0292859 0.0213629 1.0000
Verrucomicrobia patient FALSE . 1 6.661e-03 0.0120381 0.0000000 0.4000
Verrucomicrobia patient FALSE . 2 4.125e-04 0.0010915 0.0000000 0.1429
Verrucomicrobia patient FALSE . 3 1.873e-04 0.0004587 0.0000000 0.1667
Verrucomicrobia patient FALSE . 4 6.167e-05 0.0001510 0.0000000 0.1667
Verrucomicrobia patient TRUE . 1 1.355e-02 0.0485697 0.0000000 0.3077
Verrucomicrobia patient TRUE . 2 3.747e-04 0.0011850 0.0000000 0.1000
Verrucomicrobia patient TRUE . 3 8.617e-04 0.0024373 0.0000000 0.1250
Verrucomicrobia patient TRUE . 4 0.000e+00 0.0000000 0.0000000 0.0000

(1.1.1.1.6.2.4.2.1.1.1) Figure 18. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar_stacked plot. Image file: plots/3237167bf9b.svg.

(1.1.1.1.6.2.4.2.1.1.1) Figure 19. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323188a1359.svg.

(1.1.1.1.6.2.4.2.1.1.1) Figure 20. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3233b3187b9.svg.

(1.1.1.1.6.2.4.2.1.1.1) Figure 21. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/323205f32fe.svg.

(1.1.1.1.6.2.4.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.1.6.2.4.2.1.2.1) Figure 22. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323a4454bc.svg.

(1.1.1.1.6.2.4.2.1.2.1) Figure 23. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/32327fa1548.svg.

(1.1.1.1.6.2.4.2.1.2.1) Figure 24. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3234a485b4a.svg.

(1.1.1.1.6.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.1.6.2.4.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.1.6.2.4.2.2.1.1) Figure 25. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3233c80ba8b.svg.

(1.1.1.1.6.2.4.2.2.1.1) Figure 26. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/323b6f737c.svg.

(1.1.1.1.6.2.4.2.2.1.1) Figure 27. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32327e12d1b.svg.

(1.1.1.1.6.2.4.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.1.6.2.4.2.2.2.1) Figure 28. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323625bc6.svg.

(1.1.1.1.6.2.4.2.2.2.1) Figure 29. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/323b84bc0b.svg.

(1.1.1.1.6.2.4.2.2.2.1) Figure 30. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32350b48d5a.svg.

(1.1.1.1.6.2.5) Grouping variables Drug.Before.Diet,Sample.type.1
(1.1.1.1.6.2.6) Iterating over Abundance. profile sorting order
(1.1.1.1.6.2.6.1) Abundance. profile sorting order: average abundance
(1.1.1.1.6.2.6.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.1.6.2.6.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.1.6.2.6.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.1.6.2.6.2.1.1.0) Table 10. Data table used for plots. Data grouped by Drug.Before.Diet,Sample.type.1. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.1.6.2.6.2.1.1.0-3231169a8fe.1.1.1.1.6.2.6.2.1.1.csv

.record.id Drug.Before.Diet Sample.type.1 feature Abundance
SM1 DrugBefore_YES patient.before.diet Bacteroidetes 0.7837908
SM10 DrugBefore_YES patient.after.diet Bacteroidetes 0.2396904
SM100 DrugBefore_YES patient.after.diet Bacteroidetes 0.5483424
SM11 DrugBefore_YES patient.after.diet Bacteroidetes 0.9085606
SM12 DrugBefore_YES patient.before.diet Bacteroidetes 0.9297539
SM13 DrugBefore_NO patient.before.diet Bacteroidetes 0.7549107
SM14 DrugBefore_NO patient.before.diet Bacteroidetes 0.0643696
SM15 DrugBefore_YES control Bacteroidetes 0.4787347
SM16 DrugBefore_NO patient.after.diet Bacteroidetes 0.3909652
SM17 DrugBefore_YES patient.before.diet Bacteroidetes 0.8191974
SM18 DrugBefore_NO patient.after.diet Bacteroidetes 0.7196575
SM19 DrugBefore_NO patient.after.diet Bacteroidetes 0.2253586
SM2 DrugBefore_NO patient.before.diet Bacteroidetes 0.8869878
SM20 DrugBefore_NO control Bacteroidetes 0.5052377
SM21 DrugBefore_NO patient.before.diet Bacteroidetes 0.5680175
SM22 DrugBefore_YES patient.before.diet Bacteroidetes 0.6115163
SM23 DrugBefore_YES patient.after.diet Bacteroidetes 0.2816259
SM24 DrugBefore_NO patient.before.diet Bacteroidetes 0.8667524
SM25 DrugBefore_NO patient.after.diet Bacteroidetes 0.4539656
SM26 DrugBefore_NO control Bacteroidetes 0.5339906
SM28 DrugBefore_NO control Bacteroidetes 0.2661871
SM29 DrugBefore_YES patient.after.diet Bacteroidetes 0.9319131
SM3 DrugBefore_YES patient.after.diet Bacteroidetes 0.3065958
SM30 DrugBefore_YES patient.after.diet Bacteroidetes 0.0706857
SM31 DrugBefore_NO control Bacteroidetes 0.5825243
SM33 DrugBefore_YES patient.before.diet Bacteroidetes 0.6904013
SM35 DrugBefore_NO control Bacteroidetes 0.6847011
SM36 DrugBefore_NO patient.after.diet Bacteroidetes 0.0003219
SM37 DrugBefore_NO control Bacteroidetes 0.4116736
SM38 DrugBefore_YES patient.after.diet Bacteroidetes 0.9844826
SM39 DrugBefore_NO patient.before.diet Bacteroidetes 0.9344382
SM40 DrugBefore_NO patient.after.diet Bacteroidetes 0.7285173
SM41 DrugBefore_YES patient.before.diet Bacteroidetes 0.5561997
SM42 DrugBefore_NO patient.after.diet Bacteroidetes 0.7113608
SM43 DrugBefore_YES patient.after.diet Bacteroidetes 0.7229302
SM44 DrugBefore_NO control Bacteroidetes 0.3689400
SM45 DrugBefore_NO patient.after.diet Bacteroidetes 0.0000000
SM48 DrugBefore_NO control Bacteroidetes 0.7198795
SM49 DrugBefore_YES patient.before.diet Bacteroidetes 0.9321676
SM5 DrugBefore_YES patient.after.diet Bacteroidetes 0.8376844
SM50 DrugBefore_NO patient.after.diet Bacteroidetes 0.0000000
SM51 DrugBefore_YES patient.after.diet Bacteroidetes 0.7147000
SM52 DrugBefore_NO patient.before.diet Bacteroidetes 0.0982678
SM53 DrugBefore_YES patient.after.diet Bacteroidetes 0.8029344
SM54 DrugBefore_YES patient.after.diet Bacteroidetes 0.8090072
SM55 DrugBefore_NO control Bacteroidetes 0.7867457
SM56 DrugBefore_YES patient.after.diet Bacteroidetes 0.7317232
SM57 DrugBefore_YES patient.before.diet Bacteroidetes 0.9046076
SM58 DrugBefore_NO patient.after.diet Bacteroidetes 0.7734046
SM59 DrugBefore_NO patient.after.diet Bacteroidetes 0.0576779
SM60 DrugBefore_YES patient.after.diet Bacteroidetes 0.8495575
SM62 DrugBefore_YES patient.before.diet Bacteroidetes 0.9714974
SM63 DrugBefore_NO control Bacteroidetes 0.6522523
SM64 DrugBefore_YES patient.after.diet Bacteroidetes 0.8682775
SM65 DrugBefore_YES patient.after.diet Bacteroidetes 0.3740898
SM66 DrugBefore_NO control Bacteroidetes 0.6462271
SM67 DrugBefore_YES patient.after.diet Bacteroidetes 0.9138286
SM68 DrugBefore_NO patient.after.diet Bacteroidetes 0.1704581
SM69 DrugBefore_YES patient.after.diet Bacteroidetes 0.8374262
SM7 DrugBefore_NO control Bacteroidetes 0.2200704
SM70 DrugBefore_NO control Bacteroidetes 0.5636549
SM71 DrugBefore_YES patient.after.diet Bacteroidetes 0.9181355
SM72 DrugBefore_NO control Bacteroidetes 0.2780423
SM73 DrugBefore_NO patient.before.diet Bacteroidetes 0.8563497
SM74 DrugBefore_NO control Bacteroidetes 0.0926350
SM75 DrugBefore_NO patient.after.diet Bacteroidetes 0.0023769
SM76 DrugBefore_NO control Bacteroidetes 0.8226714
SM77 DrugBefore_YES patient.after.diet Bacteroidetes 0.7635462
SM79 DrugBefore_NO patient.after.diet Bacteroidetes 0.8495792
SM8 DrugBefore_NO patient.before.diet Bacteroidetes 0.8249907
SM81 DrugBefore_NO control Bacteroidetes 0.0000000
SM82 DrugBefore_YES patient.after.diet Bacteroidetes 0.9557214
SM83 DrugBefore_YES patient.before.diet Bacteroidetes 0.8253707
SM84 DrugBefore_YES patient.before.diet Bacteroidetes 0.8861386
SM86 DrugBefore_YES patient.after.diet Bacteroidetes 0.0034130
SM87 DrugBefore_YES patient.before.diet Bacteroidetes 0.8668189
SM88 DrugBefore_YES patient.after.diet Bacteroidetes 0.8387042
SM89 DrugBefore_NO control Bacteroidetes 0.8860391
SM9 DrugBefore_NO patient.after.diet Bacteroidetes 0.6635130
SM90 DrugBefore_NO patient.after.diet Bacteroidetes 0.6175743
SM91 DrugBefore_YES patient.after.diet Bacteroidetes 0.7223533
SM92 DrugBefore_NO patient.after.diet Bacteroidetes 0.8864163
SM93 DrugBefore_YES patient.before.diet Bacteroidetes 0.7781065
SM95 DrugBefore_NO control Bacteroidetes 0.5376651
SM96 DrugBefore_NO patient.before.diet Bacteroidetes 0.6381524
SM98 DrugBefore_NO patient.after.diet Bacteroidetes 0.8378232
SM99 DrugBefore_NO patient.after.diet Bacteroidetes 0.6950886
SM1 DrugBefore_YES patient.before.diet Firmicutes 0.1926574
SM10 DrugBefore_YES patient.after.diet Firmicutes 0.7267041
SM100 DrugBefore_YES patient.after.diet Firmicutes 0.4106607
SM11 DrugBefore_YES patient.after.diet Firmicutes 0.0832883
SM12 DrugBefore_YES patient.before.diet Firmicutes 0.0667050
SM13 DrugBefore_NO patient.before.diet Firmicutes 0.2004464
SM14 DrugBefore_NO patient.before.diet Firmicutes 0.8985233
SM15 DrugBefore_YES control Firmicutes 0.5021584
SM16 DrugBefore_NO patient.after.diet Firmicutes 0.5901852
SM17 DrugBefore_YES patient.before.diet Firmicutes 0.1419115
SM18 DrugBefore_NO patient.after.diet Firmicutes 0.2613732
SM19 DrugBefore_NO patient.after.diet Firmicutes 0.7376215
SM2 DrugBefore_NO patient.before.diet Firmicutes 0.1035274
SM20 DrugBefore_NO control Firmicutes 0.4700510
SM21 DrugBefore_NO patient.before.diet Firmicutes 0.4124769
SM22 DrugBefore_YES patient.before.diet Firmicutes 0.3619962
SM23 DrugBefore_YES patient.after.diet Firmicutes 0.7183741
SM24 DrugBefore_NO patient.before.diet Firmicutes 0.0873312
SM25 DrugBefore_NO patient.after.diet Firmicutes 0.5346644
SM26 DrugBefore_NO control Firmicutes 0.4376724
SM28 DrugBefore_NO control Firmicutes 0.6702638
SM29 DrugBefore_YES patient.after.diet Firmicutes 0.0659983
SM3 DrugBefore_YES patient.after.diet Firmicutes 0.6836746
SM30 DrugBefore_YES patient.after.diet Firmicutes 0.6301592
SM31 DrugBefore_NO control Firmicutes 0.3685275
SM33 DrugBefore_YES patient.before.diet Firmicutes 0.0664831
SM35 DrugBefore_NO control Firmicutes 0.1777677
SM36 DrugBefore_NO patient.after.diet Firmicutes 0.9916318
SM37 DrugBefore_NO control Firmicutes 0.5380090
SM38 DrugBefore_YES patient.after.diet Firmicutes 0.0149522
SM39 DrugBefore_NO patient.before.diet Firmicutes 0.0457112
SM40 DrugBefore_NO patient.after.diet Firmicutes 0.1850893
SM41 DrugBefore_YES patient.before.diet Firmicutes 0.2222222
SM42 DrugBefore_NO patient.after.diet Firmicutes 0.2680816
SM43 DrugBefore_YES patient.after.diet Firmicutes 0.2170803
SM44 DrugBefore_NO control Firmicutes 0.5480690
SM45 DrugBefore_NO patient.after.diet Firmicutes 0.9998080
SM48 DrugBefore_NO control Firmicutes 0.2306368
SM49 DrugBefore_YES patient.before.diet Firmicutes 0.0630087
SM5 DrugBefore_YES patient.after.diet Firmicutes 0.1042550
SM50 DrugBefore_NO patient.after.diet Firmicutes 0.9071785
SM51 DrugBefore_YES patient.after.diet Firmicutes 0.2014276
SM52 DrugBefore_NO patient.before.diet Firmicutes 0.7350474
SM53 DrugBefore_YES patient.after.diet Firmicutes 0.1567175
SM54 DrugBefore_YES patient.after.diet Firmicutes 0.1867193
SM55 DrugBefore_NO control Firmicutes 0.1964930
SM56 DrugBefore_YES patient.after.diet Firmicutes 0.2457572
SM57 DrugBefore_YES patient.before.diet Firmicutes 0.0910727
SM58 DrugBefore_NO patient.after.diet Firmicutes 0.2163913
SM59 DrugBefore_NO patient.after.diet Firmicutes 0.9138577
SM60 DrugBefore_YES patient.after.diet Firmicutes 0.0667120
SM62 DrugBefore_YES patient.before.diet Firmicutes 0.0272983
SM63 DrugBefore_NO control Firmicutes 0.3144144
SM64 DrugBefore_YES patient.after.diet Firmicutes 0.0731544
SM65 DrugBefore_YES patient.after.diet Firmicutes 0.5987086
SM66 DrugBefore_NO control Firmicutes 0.3329670
SM67 DrugBefore_YES patient.after.diet Firmicutes 0.0858185
SM68 DrugBefore_NO patient.after.diet Firmicutes 0.7067622
SM69 DrugBefore_YES patient.after.diet Firmicutes 0.1394156
SM7 DrugBefore_NO control Firmicutes 0.6870599
SM70 DrugBefore_NO control Firmicutes 0.3690709
SM71 DrugBefore_YES patient.after.diet Firmicutes 0.0709753
SM72 DrugBefore_NO control Firmicutes 0.6537037
SM73 DrugBefore_NO patient.before.diet Firmicutes 0.1129618
SM74 DrugBefore_NO control Firmicutes 0.8235679
SM75 DrugBefore_NO patient.after.diet Firmicutes 0.9925297
SM76 DrugBefore_NO control Firmicutes 0.1656713
SM77 DrugBefore_YES patient.after.diet Firmicutes 0.2001802
SM79 DrugBefore_NO patient.after.diet Firmicutes 0.1429830
SM8 DrugBefore_NO patient.before.diet Firmicutes 0.1345940
SM81 DrugBefore_NO control Firmicutes 0.4655685
SM82 DrugBefore_YES patient.after.diet Firmicutes 0.0404868
SM83 DrugBefore_YES patient.before.diet Firmicutes 0.1639209
SM84 DrugBefore_YES patient.before.diet Firmicutes 0.0789167
SM86 DrugBefore_YES patient.after.diet Firmicutes 0.9748681
SM87 DrugBefore_YES patient.before.diet Firmicutes 0.0711568
SM88 DrugBefore_YES patient.after.diet Firmicutes 0.1293265
SM89 DrugBefore_NO control Firmicutes 0.0789706
SM9 DrugBefore_NO patient.after.diet Firmicutes 0.2900041
SM90 DrugBefore_NO patient.after.diet Firmicutes 0.3494224
SM91 DrugBefore_YES patient.after.diet Firmicutes 0.2239015
SM92 DrugBefore_NO patient.after.diet Firmicutes 0.0989801
SM93 DrugBefore_YES patient.before.diet Firmicutes 0.2169177
SM95 DrugBefore_NO control Firmicutes 0.3980721
SM96 DrugBefore_NO patient.before.diet Firmicutes 0.2489554
SM98 DrugBefore_NO patient.after.diet Firmicutes 0.0793432
SM99 DrugBefore_NO patient.after.diet Firmicutes 0.2789868
SM1 DrugBefore_YES patient.before.diet Proteobacteria 0.0219067
SM10 DrugBefore_YES patient.after.diet Proteobacteria 0.0063606
SM100 DrugBefore_YES patient.after.diet Proteobacteria 0.0290747
SM11 DrugBefore_YES patient.after.diet Proteobacteria 0.0032064
SM12 DrugBefore_YES patient.before.diet Proteobacteria 0.0011951
SM13 DrugBefore_NO patient.before.diet Proteobacteria 0.0049107
SM14 DrugBefore_NO patient.before.diet Proteobacteria 0.0064370
SM15 DrugBefore_YES control Proteobacteria 0.0124549
SM16 DrugBefore_NO patient.after.diet Proteobacteria 0.0053624
SM17 DrugBefore_YES patient.before.diet Proteobacteria 0.0223417
SM18 DrugBefore_NO patient.after.diet Proteobacteria 0.0167870
SM19 DrugBefore_NO patient.after.diet Proteobacteria 0.0356317
SM2 DrugBefore_NO patient.before.diet Proteobacteria 0.0056413
SM20 DrugBefore_NO control Proteobacteria 0.0021488
SM21 DrugBefore_NO patient.before.diet Proteobacteria 0.0131159
SM22 DrugBefore_YES patient.before.diet Proteobacteria 0.0122841
SM23 DrugBefore_YES patient.after.diet Proteobacteria 0.0000000
SM24 DrugBefore_NO patient.before.diet Proteobacteria 0.0415434
SM25 DrugBefore_NO patient.after.diet Proteobacteria 0.0030505
SM26 DrugBefore_NO control Proteobacteria 0.0053778
SM28 DrugBefore_NO control Proteobacteria 0.0171863
SM29 DrugBefore_YES patient.after.diet Proteobacteria 0.0000000
SM3 DrugBefore_YES patient.after.diet Proteobacteria 0.0069012
SM30 DrugBefore_YES patient.after.diet Proteobacteria 0.2575561
SM31 DrugBefore_NO control Proteobacteria 0.0024272
SM33 DrugBefore_YES patient.before.diet Proteobacteria 0.2423289

(1.1.1.1.6.2.6.2.1.1.1) Widget 6. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.1.6.2.6.2.1.1.1-323165a1376Dynamic.Pivot.Table.html

(1.1.1.1.6.2.6.2.1.1.1) Widget 7. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.1.6.2.6.2.1.1.1-323115a451Dynamic.Pivot.Table.html

(1.1.1.1.6.2.6.2.1.1.1) Table 11. Summary table. Data grouped by Drug.Before.Diet,Sample.type.1. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.1.6.2.6.2.1.1.1-3234477b3f1.1.1.1.1.6.2.6.2.1.1.csv

feature Drug.Before.Diet Sample.type.1 mean sd median incidence
Bacteroidetes DrugBefore_NO control 0.5031125 0.2470818 0.5376651 0.9474
Bacteroidetes DrugBefore_NO patient.after.diet 0.4623189 0.3373238 0.6175743 0.8947
Bacteroidetes DrugBefore_NO patient.before.diet 0.6493237 0.3201539 0.7899507 1.0000
Bacteroidetes DrugBefore_YES control 0.4787347 NA 0.4787347 1.0000
Bacteroidetes DrugBefore_YES patient.after.diet 0.6774372 0.2896039 0.8029344 1.0000
Bacteroidetes DrugBefore_YES patient.before.diet 0.8119667 0.1269555 0.8253707 1.0000
Firmicutes DrugBefore_NO control 0.4171872 0.2022691 0.3980721 1.0000
Firmicutes DrugBefore_NO patient.after.diet 0.5023628 0.3375395 0.3494224 1.0000
Firmicutes DrugBefore_NO patient.before.diet 0.2979575 0.2950437 0.1675202 1.0000
Firmicutes DrugBefore_YES control 0.5021584 NA 0.5021584 1.0000
Firmicutes DrugBefore_YES patient.after.diet 0.2819726 0.2722233 0.1867193 1.0000
Firmicutes DrugBefore_YES patient.before.diet 0.1357129 0.0936925 0.0910727 1.0000
Proteobacteria DrugBefore_NO control 0.0408313 0.0719079 0.0180772 1.0000
Proteobacteria DrugBefore_NO patient.after.diet 0.0275566 0.0323649 0.0129623 1.0000
Proteobacteria DrugBefore_NO patient.before.diet 0.0273244 0.0473340 0.0119343 1.0000
Proteobacteria DrugBefore_YES control 0.0124549 NA 0.0124549 1.0000
Proteobacteria DrugBefore_YES patient.after.diet 0.0308500 0.0523840 0.0139551 0.8800
Proteobacteria DrugBefore_YES patient.before.diet 0.0321646 0.0655164 0.0122841 0.9231
Unclassified_Bacteria DrugBefore_NO control 0.0153411 0.0138827 0.0118838 1.0000
Unclassified_Bacteria DrugBefore_NO patient.after.diet 0.0037686 0.0035311 0.0025999 0.9474
Unclassified_Bacteria DrugBefore_NO patient.before.diet 0.0148000 0.0271664 0.0044485 1.0000
Unclassified_Bacteria DrugBefore_YES control 0.0062982 NA 0.0062982 1.0000
Unclassified_Bacteria DrugBefore_YES patient.after.diet 0.0029534 0.0046391 0.0017261 0.9600
Unclassified_Bacteria DrugBefore_YES patient.before.diet 0.0038066 0.0041644 0.0022574 0.9231
Actinobacteria DrugBefore_NO control 0.0171750 0.0436518 0.0027279 0.9474
Actinobacteria DrugBefore_NO patient.after.diet 0.0022218 0.0047316 0.0004114 0.6842
Actinobacteria DrugBefore_NO patient.before.diet 0.0034710 0.0076244 0.0008172 1.0000
Actinobacteria DrugBefore_YES control 0.0003538 NA 0.0003538 1.0000
Actinobacteria DrugBefore_YES patient.after.diet 0.0033735 0.0063331 0.0004177 0.7600
Actinobacteria DrugBefore_YES patient.before.diet 0.0027821 0.0059632 0.0006927 0.7692
Verrucomicrobia DrugBefore_NO control 0.0046650 0.0103270 0.0000000 0.4737
Verrucomicrobia DrugBefore_NO patient.after.diet 0.0002306 0.0006964 0.0000000 0.1579
Verrucomicrobia DrugBefore_NO patient.before.diet 0.0066615 0.0120381 0.0000000 0.4000
Verrucomicrobia DrugBefore_YES control 0.0000000 NA 0.0000000 0.0000
Verrucomicrobia DrugBefore_YES patient.after.diet 0.0004256 0.0015416 0.0000000 0.0800
Verrucomicrobia DrugBefore_YES patient.before.diet 0.0135531 0.0485697 0.0000000 0.3077

(1.1.1.1.6.2.6.2.1.1.1) Figure 31. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar_stacked plot. Image file: plots/32368e64947.svg.

(1.1.1.1.6.2.6.2.1.1.1) Figure 32. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3232e6db706.svg.

(1.1.1.1.6.2.6.2.1.1.1) Figure 33. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/323c15247.svg.

(1.1.1.1.6.2.6.2.1.1.1) Figure 34. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/323450cc12c.svg.

(1.1.1.1.6.2.6.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.1.6.2.6.2.1.2.1) Figure 35. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/32348b594a5.svg.

(1.1.1.1.6.2.6.2.1.2.1) Figure 36. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/323543155e9.svg.

(1.1.1.1.6.2.6.2.1.2.1) Figure 37. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3232f5df00c.svg.

(1.1.1.1.6.2.6.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.1.6.2.6.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.1.6.2.6.2.2.1.1) Figure 38. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3235859d5af.svg.

(1.1.1.1.6.2.6.2.2.1.1) Figure 39. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/32340e5c1fc.svg.

(1.1.1.1.6.2.6.2.2.1.1) Figure 40. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3233038a48f.svg.

(1.1.1.1.6.2.6.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.1.6.2.6.2.2.2.1) Figure 41. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/323462bf45.svg.

(1.1.1.1.6.2.6.2.2.2.1) Figure 42. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3234ae93bb3.svg.

(1.1.1.1.6.2.6.2.2.2.1) Figure 43. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32343258ad3.svg.

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